Contacts of the strand formed by residues 127 - 134 (chain F) in PDB entry 1H4O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 127 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F GLY 3.4 6.5 - - - +
39F VAL* 4.0 0.4 - - - +
40F PRO* 3.7 11.4 - - + +
46F GLY* 4.3 1.2 - - - -
47F CYS* 3.3 22.8 - - - +
51F HIS* 3.1 43.0 + - + +
125F LEU 3.7 1.4 + - - -
126F LYS* 1.3 71.1 - - - +
128F PHE* 1.3 58.7 + - - +
142F VAL* 3.8 3.1 - - - +
143F GLU* 3.0 35.4 + - + +
146F GLY 2.9 13.9 + - - +
147F THR* 3.0 17.1 + - - -
148F GLY 2.8 26.9 + - - -
149F LEU* 3.5 19.9 - - - +
152F SER* 3.1 20.0 - - - +
1162F BEZ 3.1 31.9 + - - -
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Residues in contact with PHE 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 3.9 22.9 - - + -
37F PHE* 3.2 9.5 - - - +
38F GLY* 2.9 50.2 + - - +
51F HIS* 4.0 2.8 - - - -
73F LEU* 4.9 2.7 - - + -
104F PHE* 3.8 20.4 - + - -
110F LEU* 4.1 21.1 - - + -
125F LEU* 4.3 16.4 - - + -
126F LYS 3.4 20.0 - - - +
127F ARG* 1.3 75.7 - - - +
129F SER* 1.3 71.9 + - - +
130F MET* 3.6 28.0 - - + -
140F LEU* 4.6 1.6 - - + -
141F ASN 3.0 14.1 - - - +
142F VAL* 4.1 16.2 - - + -
152F SER* 3.7 6.3 - - - -
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Residues in contact with SER 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F VAL* 5.2 0.2 - - - -
36F LEU 3.4 7.2 - - - -
37F PHE* 4.0 9.4 - - - -
55F PHE* 4.5 4.5 - - - -
128F PHE* 1.3 77.8 - - - +
130F MET* 1.3 64.4 + - - +
140F LEU* 3.6 3.1 - - - +
141F ASN* 2.8 59.2 + - - +
151F CYS 3.9 0.2 + - - -
152F SER* 3.5 23.2 + - - -
157F ILE* 3.6 15.0 - - - +
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Residues in contact with MET 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F ILE* 4.6 7.6 - - + -
9F ILE* 3.9 26.2 - - - -
35F VAL* 3.2 9.2 - - - +
36F LEU* 2.7 56.4 + - + +
104F PHE* 4.4 11.7 - - + -
110F LEU* 4.5 6.7 - - + -
128F PHE* 3.6 20.9 - - + -
129F SER* 1.3 76.7 - - - +
131F VAL* 1.3 61.0 + - - +
132F VAL* 3.8 6.1 - - + -
137F VAL* 4.0 21.8 - - + -
139F ALA 3.2 13.7 - - - +
140F LEU* 3.8 20.6 - - + -
157F ILE* 3.8 6.1 - - - -
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Residues in contact with VAL 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LYS* 4.3 14.4 - - + -
34F GLY 3.5 8.3 - - - +
35F VAL* 4.6 2.5 - - + +
130F MET* 1.3 72.6 - - - +
132F VAL* 1.3 64.6 + - - +
133F GLN* 4.8 0.4 - - + +
137F VAL* 3.6 4.9 - - - +
138F LYS* 2.8 41.4 + - + -
139F ALA* 3.0 27.5 + - + +
157F ILE* 3.5 30.2 - - + +
160F GLN* 5.0 5.2 - - + +
161F LEU* 3.7 30.5 - - + -
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Residues in contact with VAL 132 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F ILE* 4.5 13.9 - - + -
29F PHE* 3.7 32.5 - - + -
32F LYS 3.7 2.1 - - - +
33F LYS* 3.5 1.7 - - - +
34F GLY* 2.8 41.3 + - - +
36F LEU* 4.5 8.3 - - + +
130F MET* 3.8 32.5 - - + +
131F VAL* 1.3 78.2 - - - +
133F GLN* 1.3 61.8 + - - +
134F ASP 4.1 0.2 - - - -
135F GLY* 3.6 27.1 - - - +
136F ILE 3.3 6.3 - - - +
137F VAL* 4.9 2.5 - - + -
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Residues in contact with GLN 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ASP* 2.9 35.3 + - + +
148E GLY* 5.0 6.3 - - - -
150E THR* 6.0 4.0 - - - +
32F LYS 3.7 1.1 - - - -
33F LYS* 4.3 23.4 - - + +
131F VAL* 4.2 1.1 - - + -
132F VAL* 1.3 72.9 - - - +
134F ASP* 1.3 76.3 + - + +
135F GLY 3.1 0.4 - - - -
136F ILE* 2.8 28.2 + - - +
138F LYS* 3.6 36.5 - - + +
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Residues in contact with ASP 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E PRO* 3.9 25.4 - - + +
145E ASP* 5.2 1.3 - - + -
29F PHE 3.4 10.1 - - - -
30F LYS* 3.6 9.9 - - - +
31F GLY* 2.5 36.9 + - - +
32F LYS 2.8 16.4 + - - +
133F GLN* 1.3 77.8 - - + +
135F GLY* 1.3 56.5 + - - +
136F ILE* 3.5 9.4 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il